BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716682.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 727,339 number of mapped reads = 632,566 (86.97%) number of supplementary alignments = 2,039 (0.28%) number of secondary alignments = 0 number of mapped bases = 35,720,953 bp number of sequenced bases = 35,710,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,822 duplication rate = 1.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4488 >>>>>>> ACTG content number of A's = 8,386,203 bp (23.48%) number of C's = 6,510,392 bp (18.23%) number of T's = 11,720,165 bp (32.82%) number of G's = 9,093,099 bp (25.46%) number of N's = 293 bp (0%) GC percentage = 43.69% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 185,011 number of insertions = 2,599 mapped reads with insertion percentage = 0.41% number of deletions = 6,851 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.57% >>>>>>> Coverage mean coverageData = 0.0115X std coverageData = 0.1296X There is a 1.1% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3006269 0.012061229729092631 0.15080642714188042 chr2 243199373 2808629 0.01154866875417479 0.17567311501530186 chr3 198022430 2072390 0.010465430608037686 0.1077812984403266 chr4 191154276 2216528 0.011595492637580338 0.11453235181318283 chr5 180915260 2029753 0.011219357615272476 0.10943878143773282 chr6 171115067 1907247 0.011145991019014123 0.11893211178045122 chr7 159138663 2040090 0.012819574838328258 0.16608896826452635 chr8 146364022 1869841 0.012775277520045192 0.12942799192877183 chr9 141213431 1170327 0.00828764651996877 0.10102053766546903 chr10 135534747 1588598 0.011720964809120129 0.1463361581716396 chr11 135006516 1269492 0.009403190583778934 0.11237875071373388 chr12 133851895 1792267 0.01338992623152627 0.12008508529783289 chr13 115169878 1095065 0.009508258748003536 0.10114051489516251 chr14 107349540 1190388 0.011088897073988394 0.11137423055825552 chr15 102531392 1310397 0.012780446792334586 0.1185950626190734 chr16 90354753 1230772 0.013621552371461853 0.12529204617347842 chr17 81195210 1560873 0.01922370790099564 0.1469569107087928 chr18 78077248 666624 0.008538005847747093 0.13809819718310226 chr19 59128983 933870 0.01579377747795865 0.1506095607223511 chr20 63025520 1131001 0.017945127624492428 0.14142873230117828 chr21 48129895 442667 0.009197339823824672 0.102611672047801 chr22 51304566 320512 0.006247241229952126 0.08206487779038277 chrMT 16571 3405 0.2054794520547945 0.43815810805454586 chrX 155270560 1959362 0.012619018054678233 0.1211820336128999 chrY 59373566 104586 0.0017614909638407098 0.06035141311953258